Multiple sequence alignment - TraesCS6A01G207300

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6A01G207300 chr6A 100.000 5620 0 0 1 5620 367768826 367774445 0.000000e+00 10379.0
1 TraesCS6A01G207300 chr6A 92.419 554 32 6 5072 5620 117418873 117418325 0.000000e+00 782.0
2 TraesCS6A01G207300 chr6A 87.657 559 48 14 5073 5620 609628835 609628287 1.030000e-176 630.0
3 TraesCS6A01G207300 chr6A 96.061 330 12 1 3868 4196 53585670 53585999 2.300000e-148 536.0
4 TraesCS6A01G207300 chr6A 86.028 501 33 15 23 491 34076719 34076224 2.340000e-138 503.0
5 TraesCS6A01G207300 chr6A 92.899 338 24 0 3879 4216 209390402 209390065 5.060000e-135 492.0
6 TraesCS6A01G207300 chr6D 96.787 3392 59 12 501 3870 262014778 262018141 0.000000e+00 5614.0
7 TraesCS6A01G207300 chr6D 93.516 910 16 14 4194 5074 262018131 262019026 0.000000e+00 1314.0
8 TraesCS6A01G207300 chr6B 96.008 3382 77 16 510 3870 374327826 374331170 0.000000e+00 5445.0
9 TraesCS6A01G207300 chr6B 94.692 697 16 6 4194 4890 374331160 374331835 0.000000e+00 1062.0
10 TraesCS6A01G207300 chr6B 91.477 352 27 3 3869 4217 55267271 55266920 1.100000e-131 481.0
11 TraesCS6A01G207300 chr2A 95.091 550 20 2 5072 5619 434979128 434978584 0.000000e+00 859.0
12 TraesCS6A01G207300 chr2A 89.892 554 43 8 5073 5620 83613308 83612762 0.000000e+00 701.0
13 TraesCS6A01G207300 chr2A 87.946 448 36 6 57 491 175031362 175030920 3.880000e-141 512.0
14 TraesCS6A01G207300 chr2A 93.567 342 21 1 3869 4209 27651079 27650738 5.020000e-140 508.0
15 TraesCS6A01G207300 chr2A 92.416 356 25 2 3856 4210 119297067 119297421 1.810000e-139 507.0
16 TraesCS6A01G207300 chr3A 92.377 551 32 5 5073 5620 283109482 283108939 0.000000e+00 776.0
17 TraesCS6A01G207300 chr3A 92.941 340 20 4 3880 4216 343592687 343592349 5.060000e-135 492.0
18 TraesCS6A01G207300 chr3A 94.231 52 2 1 5071 5122 53223938 53223988 1.680000e-10 78.7
19 TraesCS6A01G207300 chr1A 89.771 567 33 8 5072 5620 530149350 530149909 0.000000e+00 702.0
20 TraesCS6A01G207300 chr1A 89.587 557 42 8 5073 5620 461066166 461065617 0.000000e+00 693.0
21 TraesCS6A01G207300 chr4A 89.617 549 46 10 5073 5612 626940872 626941418 0.000000e+00 688.0
22 TraesCS6A01G207300 chr4A 93.333 345 21 2 3872 4215 682026096 682026439 5.020000e-140 508.0
23 TraesCS6A01G207300 chr1B 91.068 515 35 5 5107 5620 360985339 360985843 0.000000e+00 686.0
24 TraesCS6A01G207300 chr5A 91.767 498 24 6 1 491 115997609 115998096 0.000000e+00 676.0
25 TraesCS6A01G207300 chr5D 90.800 500 31 8 1 491 431181317 431181810 0.000000e+00 654.0
26 TraesCS6A01G207300 chr5D 94.880 332 17 0 3879 4210 35155175 35154844 2.320000e-143 520.0
27 TraesCS6A01G207300 chr5D 92.593 108 8 0 1 108 431181269 431181376 7.540000e-34 156.0
28 TraesCS6A01G207300 chr5B 91.631 466 24 8 47 504 322287600 322288058 1.030000e-176 630.0
29 TraesCS6A01G207300 chr5B 93.333 345 22 1 3864 4208 423739154 423738811 5.020000e-140 508.0
30 TraesCS6A01G207300 chr4B 91.868 455 22 6 47 491 595724852 595725301 6.180000e-174 621.0
31 TraesCS6A01G207300 chr4B 92.958 71 5 0 1 71 595724781 595724851 2.770000e-18 104.0
32 TraesCS6A01G207300 chr3B 92.035 452 21 6 50 491 7318663 7318217 6.180000e-174 621.0
33 TraesCS6A01G207300 chr3B 93.162 351 22 2 3861 4211 797669964 797669616 1.080000e-141 514.0
34 TraesCS6A01G207300 chr3D 89.400 500 38 8 1 492 376078412 376078904 2.880000e-172 616.0
35 TraesCS6A01G207300 chr3D 91.691 349 28 1 3868 4215 8000060 8000408 3.040000e-132 483.0
36 TraesCS6A01G207300 chr3D 92.593 108 8 0 1 108 376078364 376078471 7.540000e-34 156.0
37 TraesCS6A01G207300 chr2B 91.111 450 30 4 47 491 33482507 33482951 8.060000e-168 601.0
38 TraesCS6A01G207300 chr2D 93.671 395 16 5 46 437 13522681 13523069 2.920000e-162 582.0
39 TraesCS6A01G207300 chr2D 92.486 346 23 3 3874 4217 14100849 14100505 5.060000e-135 492.0
40 TraesCS6A01G207300 chr2D 95.455 66 3 0 1 66 13522612 13522677 7.700000e-19 106.0
41 TraesCS6A01G207300 chr7D 95.252 337 16 0 3872 4208 548476581 548476245 8.290000e-148 534.0
42 TraesCS6A01G207300 chr7D 91.549 355 28 2 3863 4215 298354052 298354406 6.540000e-134 488.0
43 TraesCS6A01G207300 chr7A 93.787 338 19 2 3880 4217 35382327 35382662 1.810000e-139 507.0
44 TraesCS6A01G207300 chr7A 91.736 363 24 6 3851 4208 521210659 521211020 3.020000e-137 499.0
45 TraesCS6A01G207300 chr7B 87.391 460 33 13 48 491 33410219 33409769 6.500000e-139 505.0
46 TraesCS6A01G207300 chr7B 81.443 194 33 3 8 200 240327252 240327443 7.540000e-34 156.0
47 TraesCS6A01G207300 chr7B 86.170 94 11 2 108 200 240327927 240328019 3.580000e-17 100.0
48 TraesCS6A01G207300 chr1D 92.529 348 25 1 3870 4216 15302806 15303153 1.090000e-136 497.0
49 TraesCS6A01G207300 chr1D 96.685 181 6 0 2513 2693 254865970 254866150 9.150000e-78 302.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G207300 chr6A 367768826 367774445 5619 False 10379.0 10379 100.0000 1 5620 1 chr6A.!!$F2 5619
1 TraesCS6A01G207300 chr6A 117418325 117418873 548 True 782.0 782 92.4190 5072 5620 1 chr6A.!!$R2 548
2 TraesCS6A01G207300 chr6A 609628287 609628835 548 True 630.0 630 87.6570 5073 5620 1 chr6A.!!$R4 547
3 TraesCS6A01G207300 chr6D 262014778 262019026 4248 False 3464.0 5614 95.1515 501 5074 2 chr6D.!!$F1 4573
4 TraesCS6A01G207300 chr6B 374327826 374331835 4009 False 3253.5 5445 95.3500 510 4890 2 chr6B.!!$F1 4380
5 TraesCS6A01G207300 chr2A 434978584 434979128 544 True 859.0 859 95.0910 5072 5619 1 chr2A.!!$R4 547
6 TraesCS6A01G207300 chr2A 83612762 83613308 546 True 701.0 701 89.8920 5073 5620 1 chr2A.!!$R2 547
7 TraesCS6A01G207300 chr3A 283108939 283109482 543 True 776.0 776 92.3770 5073 5620 1 chr3A.!!$R1 547
8 TraesCS6A01G207300 chr1A 530149350 530149909 559 False 702.0 702 89.7710 5072 5620 1 chr1A.!!$F1 548
9 TraesCS6A01G207300 chr1A 461065617 461066166 549 True 693.0 693 89.5870 5073 5620 1 chr1A.!!$R1 547
10 TraesCS6A01G207300 chr4A 626940872 626941418 546 False 688.0 688 89.6170 5073 5612 1 chr4A.!!$F1 539
11 TraesCS6A01G207300 chr1B 360985339 360985843 504 False 686.0 686 91.0680 5107 5620 1 chr1B.!!$F1 513
12 TraesCS6A01G207300 chr5D 431181269 431181810 541 False 405.0 654 91.6965 1 491 2 chr5D.!!$F1 490
13 TraesCS6A01G207300 chr4B 595724781 595725301 520 False 362.5 621 92.4130 1 491 2 chr4B.!!$F1 490
14 TraesCS6A01G207300 chr3D 376078364 376078904 540 False 386.0 616 90.9965 1 492 2 chr3D.!!$F2 491

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
583 643 0.251653 TTACGCACCCTGTCTCTCCT 60.252 55.000 0.00 0.0 0.00 3.69 F
609 671 1.133792 CCCCAGTCTCTCTCTCTCTCC 60.134 61.905 0.00 0.0 0.00 3.71 F
1235 1301 1.169577 CAGCGTCTCTAGTGTGGAGT 58.830 55.000 0.00 0.0 33.06 3.85 F
2361 2443 0.949105 GGTGGTCTGTGGTACAAGCG 60.949 60.000 0.00 0.0 44.16 4.68 F
3829 3915 0.035820 GGGATCGGTGCACAGGTAAA 60.036 55.000 20.43 0.0 0.00 2.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2341 2423 0.107831 GCTTGTACCACAGACCACCA 59.892 55.000 0.00 0.00 0.00 4.17 R
2361 2443 3.125829 TGAAGCTCGTCAAATTGATCTGC 59.874 43.478 0.00 4.16 0.00 4.26 R
2950 3036 1.523938 GGGTAAGCGAGCCATGGAC 60.524 63.158 18.40 7.03 45.84 4.02 R
3999 4085 0.251564 CCAATGGCAGTGGTGGGTAA 60.252 55.000 25.07 0.00 0.00 2.85 R
5058 5173 1.338973 TCGGTAAGTGCTTGAACTCGT 59.661 47.619 0.00 0.00 0.00 4.18 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 2.364448 GACCTCCTTCCGCCTCCT 60.364 66.667 0.00 0.00 0.00 3.69
66 67 2.203938 TGGAACTCCCTCCGCCTT 60.204 61.111 0.00 0.00 38.44 4.35
258 311 0.863956 AGGAGAGTAGGGAGGGGATG 59.136 60.000 0.00 0.00 0.00 3.51
336 390 1.063114 ACGTCCTAGCAGGGGTAAGAT 60.063 52.381 2.86 0.00 35.59 2.40
363 417 5.355910 ACATTTCCAGTCACAGTTAACGTTT 59.644 36.000 5.91 0.00 0.00 3.60
474 534 9.796120 AGAGAACTAGATTTTAAGAATGAGTCG 57.204 33.333 0.00 0.00 0.00 4.18
492 552 4.612943 AGTCGAATAAGGAATTCTCTCGC 58.387 43.478 5.23 4.29 41.68 5.03
493 553 3.736759 GTCGAATAAGGAATTCTCTCGCC 59.263 47.826 5.23 0.00 41.68 5.54
494 554 3.383505 TCGAATAAGGAATTCTCTCGCCA 59.616 43.478 5.23 0.00 41.68 5.69
495 555 4.119862 CGAATAAGGAATTCTCTCGCCAA 58.880 43.478 5.23 0.00 41.68 4.52
496 556 4.752101 CGAATAAGGAATTCTCTCGCCAAT 59.248 41.667 5.23 0.00 41.68 3.16
497 557 5.926542 CGAATAAGGAATTCTCTCGCCAATA 59.073 40.000 5.23 0.00 41.68 1.90
498 558 6.423905 CGAATAAGGAATTCTCTCGCCAATAA 59.576 38.462 5.23 0.00 41.68 1.40
499 559 7.042051 CGAATAAGGAATTCTCTCGCCAATAAA 60.042 37.037 5.23 0.00 41.68 1.40
583 643 0.251653 TTACGCACCCTGTCTCTCCT 60.252 55.000 0.00 0.00 0.00 3.69
604 666 2.241176 TCTCTTCCCCAGTCTCTCTCTC 59.759 54.545 0.00 0.00 0.00 3.20
605 667 2.242196 CTCTTCCCCAGTCTCTCTCTCT 59.758 54.545 0.00 0.00 0.00 3.10
606 668 2.241176 TCTTCCCCAGTCTCTCTCTCTC 59.759 54.545 0.00 0.00 0.00 3.20
607 669 1.979809 TCCCCAGTCTCTCTCTCTCT 58.020 55.000 0.00 0.00 0.00 3.10
608 670 1.843851 TCCCCAGTCTCTCTCTCTCTC 59.156 57.143 0.00 0.00 0.00 3.20
609 671 1.133792 CCCCAGTCTCTCTCTCTCTCC 60.134 61.905 0.00 0.00 0.00 3.71
610 672 1.133792 CCCAGTCTCTCTCTCTCTCCC 60.134 61.905 0.00 0.00 0.00 4.30
611 673 1.846439 CCAGTCTCTCTCTCTCTCCCT 59.154 57.143 0.00 0.00 0.00 4.20
612 674 2.242196 CCAGTCTCTCTCTCTCTCCCTT 59.758 54.545 0.00 0.00 0.00 3.95
613 675 3.309121 CCAGTCTCTCTCTCTCTCCCTTT 60.309 52.174 0.00 0.00 0.00 3.11
925 990 8.279970 TGAATATTTTGGTTCGAGATGTTGAT 57.720 30.769 0.00 0.00 0.00 2.57
930 995 3.857052 TGGTTCGAGATGTTGATGTACC 58.143 45.455 0.00 0.00 0.00 3.34
999 1064 1.204786 TTTTGGAGGGGAGCATCGGA 61.205 55.000 0.00 0.00 34.37 4.55
1166 1231 1.595382 GCGCATAGGAATCCACGCT 60.595 57.895 17.44 0.00 42.81 5.07
1235 1301 1.169577 CAGCGTCTCTAGTGTGGAGT 58.830 55.000 0.00 0.00 33.06 3.85
1333 1399 1.278699 TGCCCCGTTTTAAGATACCGT 59.721 47.619 0.00 0.00 0.00 4.83
1343 1409 8.925700 CCGTTTTAAGATACCGTAATATAACCC 58.074 37.037 0.00 0.00 0.00 4.11
1644 1711 3.557577 TGCTTGGAAAATGATGACACG 57.442 42.857 0.00 0.00 0.00 4.49
1903 1985 9.941325 TTGATGGCTTATTTGTTATTGTTGATT 57.059 25.926 0.00 0.00 0.00 2.57
1955 2037 4.956075 GGTATTTTCCTGACATTGGATGGT 59.044 41.667 0.00 0.00 33.09 3.55
2253 2335 4.819630 AGTTATGGTGTTATATGGGCAACG 59.180 41.667 0.00 0.00 37.60 4.10
2292 2374 6.128486 TGTCAAAAGTATGGATATGGCATGT 58.872 36.000 10.98 2.44 0.00 3.21
2341 2423 5.701750 TGCAAAAGCAAAAATGCACAGATAT 59.298 32.000 3.41 0.00 43.32 1.63
2361 2443 0.949105 GGTGGTCTGTGGTACAAGCG 60.949 60.000 0.00 0.00 44.16 4.68
2406 2488 2.418368 TGGTCTGAGCAACTTGTTGT 57.582 45.000 7.15 2.64 0.00 3.32
2523 2609 9.836864 TGTCTGATCTACATTATATGCAACTTT 57.163 29.630 0.00 0.00 0.00 2.66
2668 2754 5.295292 CCAACAAACATCTCTGCGATAGAAT 59.705 40.000 0.00 0.00 34.32 2.40
2950 3036 2.440627 TGAGATTGTGGATGAGGATGGG 59.559 50.000 0.00 0.00 0.00 4.00
3180 3266 4.880886 ACAAAAGACTTGGCATTTTTGC 57.119 36.364 18.53 0.00 41.71 3.68
3430 3516 6.698380 TGGTGAAAGTAAGATACTGAAGACC 58.302 40.000 0.00 0.00 39.39 3.85
3755 3841 1.992170 ACTTACAAGACGATGGACGC 58.008 50.000 0.00 0.00 46.94 5.19
3829 3915 0.035820 GGGATCGGTGCACAGGTAAA 60.036 55.000 20.43 0.00 0.00 2.01
3908 3994 6.709018 ACCAATATAAAAAGACCCGAATGG 57.291 37.500 0.00 0.00 41.37 3.16
3918 4004 4.984194 CCGAATGGGCAGATCCAA 57.016 55.556 0.00 0.00 40.62 3.53
3919 4005 3.189568 CCGAATGGGCAGATCCAAA 57.810 52.632 0.00 0.00 40.62 3.28
3920 4006 0.740737 CCGAATGGGCAGATCCAAAC 59.259 55.000 0.00 0.00 40.62 2.93
3921 4007 0.740737 CGAATGGGCAGATCCAAACC 59.259 55.000 0.00 0.00 40.62 3.27
3922 4008 1.851304 GAATGGGCAGATCCAAACCA 58.149 50.000 0.00 0.00 40.62 3.67
3923 4009 2.391678 GAATGGGCAGATCCAAACCAT 58.608 47.619 3.70 3.70 43.39 3.55
3924 4010 2.077687 ATGGGCAGATCCAAACCATC 57.922 50.000 3.70 0.00 37.35 3.51
3925 4011 1.002069 TGGGCAGATCCAAACCATCT 58.998 50.000 0.00 0.00 36.21 2.90
3926 4012 1.358787 TGGGCAGATCCAAACCATCTT 59.641 47.619 0.00 0.00 36.21 2.40
3927 4013 1.753073 GGGCAGATCCAAACCATCTTG 59.247 52.381 0.00 0.00 36.21 3.02
3928 4014 2.621407 GGGCAGATCCAAACCATCTTGA 60.621 50.000 0.00 0.00 36.21 3.02
3929 4015 2.424956 GGCAGATCCAAACCATCTTGAC 59.575 50.000 0.00 0.00 34.01 3.18
3930 4016 2.424956 GCAGATCCAAACCATCTTGACC 59.575 50.000 0.00 0.00 0.00 4.02
3931 4017 2.679837 CAGATCCAAACCATCTTGACCG 59.320 50.000 0.00 0.00 0.00 4.79
3932 4018 2.305927 AGATCCAAACCATCTTGACCGT 59.694 45.455 0.00 0.00 0.00 4.83
3933 4019 2.178912 TCCAAACCATCTTGACCGTC 57.821 50.000 0.00 0.00 0.00 4.79
3934 4020 1.418264 TCCAAACCATCTTGACCGTCA 59.582 47.619 0.00 0.00 0.00 4.35
3935 4021 2.158740 TCCAAACCATCTTGACCGTCAA 60.159 45.455 13.29 13.29 34.79 3.18
3936 4022 2.621055 CCAAACCATCTTGACCGTCAAA 59.379 45.455 14.74 6.94 35.73 2.69
3937 4023 3.255642 CCAAACCATCTTGACCGTCAAAT 59.744 43.478 14.74 8.71 35.73 2.32
3938 4024 4.475944 CAAACCATCTTGACCGTCAAATC 58.524 43.478 14.74 0.00 35.73 2.17
3939 4025 3.417069 ACCATCTTGACCGTCAAATCA 57.583 42.857 14.74 3.04 35.73 2.57
3940 4026 3.955471 ACCATCTTGACCGTCAAATCAT 58.045 40.909 14.74 5.10 35.73 2.45
3941 4027 3.691118 ACCATCTTGACCGTCAAATCATG 59.309 43.478 14.74 14.86 35.73 3.07
3942 4028 3.691118 CCATCTTGACCGTCAAATCATGT 59.309 43.478 14.74 0.00 35.73 3.21
3943 4029 4.156556 CCATCTTGACCGTCAAATCATGTT 59.843 41.667 14.74 0.00 35.73 2.71
3944 4030 5.353956 CCATCTTGACCGTCAAATCATGTTA 59.646 40.000 14.74 0.00 35.73 2.41
3945 4031 6.038603 CCATCTTGACCGTCAAATCATGTTAT 59.961 38.462 14.74 0.00 35.73 1.89
3946 4032 6.662414 TCTTGACCGTCAAATCATGTTATC 57.338 37.500 14.74 0.00 35.73 1.75
3947 4033 6.406370 TCTTGACCGTCAAATCATGTTATCT 58.594 36.000 14.74 0.00 35.73 1.98
3948 4034 7.552459 TCTTGACCGTCAAATCATGTTATCTA 58.448 34.615 14.74 0.00 35.73 1.98
3949 4035 8.038351 TCTTGACCGTCAAATCATGTTATCTAA 58.962 33.333 14.74 0.00 35.73 2.10
3950 4036 7.534085 TGACCGTCAAATCATGTTATCTAAC 57.466 36.000 0.00 0.00 36.74 2.34
3951 4037 6.254804 TGACCGTCAAATCATGTTATCTAACG 59.745 38.462 0.00 0.00 39.00 3.18
3952 4038 5.974300 CCGTCAAATCATGTTATCTAACGG 58.026 41.667 0.00 0.00 39.00 4.44
3953 4039 5.522460 CCGTCAAATCATGTTATCTAACGGT 59.478 40.000 12.97 0.00 40.62 4.83
3954 4040 6.036735 CCGTCAAATCATGTTATCTAACGGTT 59.963 38.462 0.00 0.00 40.62 4.44
3955 4041 6.899771 CGTCAAATCATGTTATCTAACGGTTG 59.100 38.462 3.07 0.00 39.00 3.77
3956 4042 7.201487 CGTCAAATCATGTTATCTAACGGTTGA 60.201 37.037 3.07 0.00 39.00 3.18
3957 4043 8.447833 GTCAAATCATGTTATCTAACGGTTGAA 58.552 33.333 3.07 0.00 39.00 2.69
3958 4044 9.004717 TCAAATCATGTTATCTAACGGTTGAAA 57.995 29.630 3.07 0.00 39.00 2.69
3959 4045 9.787532 CAAATCATGTTATCTAACGGTTGAAAT 57.212 29.630 3.07 0.00 39.00 2.17
3961 4047 7.229228 TCATGTTATCTAACGGTTGAAATCG 57.771 36.000 3.07 0.00 39.00 3.34
3962 4048 5.459110 TGTTATCTAACGGTTGAAATCGC 57.541 39.130 3.07 0.00 39.00 4.58
3963 4049 5.172934 TGTTATCTAACGGTTGAAATCGCT 58.827 37.500 3.07 0.00 39.00 4.93
3964 4050 5.640357 TGTTATCTAACGGTTGAAATCGCTT 59.360 36.000 3.07 0.00 39.00 4.68
3965 4051 4.859629 ATCTAACGGTTGAAATCGCTTC 57.140 40.909 3.07 0.00 34.31 3.86
3966 4052 3.655486 TCTAACGGTTGAAATCGCTTCA 58.345 40.909 3.07 0.00 42.48 3.02
3975 4061 3.825308 TGAAATCGCTTCAATGTTGAGC 58.175 40.909 0.00 2.30 41.21 4.26
3976 4062 3.252944 TGAAATCGCTTCAATGTTGAGCA 59.747 39.130 13.55 5.58 41.21 4.26
3977 4063 2.907910 ATCGCTTCAATGTTGAGCAC 57.092 45.000 13.55 0.00 38.61 4.40
3978 4064 0.874390 TCGCTTCAATGTTGAGCACC 59.126 50.000 13.55 0.00 38.61 5.01
3979 4065 0.592637 CGCTTCAATGTTGAGCACCA 59.407 50.000 13.55 0.00 38.61 4.17
3980 4066 1.001487 CGCTTCAATGTTGAGCACCAA 60.001 47.619 13.55 0.00 38.61 3.67
3981 4067 2.543445 CGCTTCAATGTTGAGCACCAAA 60.543 45.455 13.55 0.00 38.61 3.28
3982 4068 2.796593 GCTTCAATGTTGAGCACCAAAC 59.203 45.455 10.31 0.00 38.61 2.93
3983 4069 3.737663 GCTTCAATGTTGAGCACCAAACA 60.738 43.478 10.31 0.00 38.61 2.83
3984 4070 4.624015 CTTCAATGTTGAGCACCAAACAT 58.376 39.130 0.00 0.00 38.61 2.71
3985 4071 3.979948 TCAATGTTGAGCACCAAACATG 58.020 40.909 2.08 0.00 36.36 3.21
3986 4072 3.384146 TCAATGTTGAGCACCAAACATGT 59.616 39.130 0.00 0.00 36.36 3.21
3987 4073 4.121317 CAATGTTGAGCACCAAACATGTT 58.879 39.130 4.92 4.92 36.36 2.71
3988 4074 3.883830 TGTTGAGCACCAAACATGTTT 57.116 38.095 18.13 18.13 36.36 2.83
3989 4075 4.991153 TGTTGAGCACCAAACATGTTTA 57.009 36.364 22.87 3.58 36.36 2.01
3990 4076 5.330455 TGTTGAGCACCAAACATGTTTAA 57.670 34.783 22.87 9.60 36.36 1.52
3991 4077 5.105752 TGTTGAGCACCAAACATGTTTAAC 58.894 37.500 22.87 19.86 36.36 2.01
3992 4078 3.958704 TGAGCACCAAACATGTTTAACG 58.041 40.909 22.87 15.18 0.00 3.18
3993 4079 2.724174 GAGCACCAAACATGTTTAACGC 59.276 45.455 22.87 22.01 0.00 4.84
3994 4080 2.360801 AGCACCAAACATGTTTAACGCT 59.639 40.909 22.87 23.59 0.00 5.07
3995 4081 2.724174 GCACCAAACATGTTTAACGCTC 59.276 45.455 22.87 7.44 0.00 5.03
3996 4082 3.550030 GCACCAAACATGTTTAACGCTCT 60.550 43.478 22.87 0.00 0.00 4.09
3997 4083 4.319911 GCACCAAACATGTTTAACGCTCTA 60.320 41.667 22.87 0.00 0.00 2.43
3998 4084 5.753744 CACCAAACATGTTTAACGCTCTAA 58.246 37.500 22.87 0.00 0.00 2.10
3999 4085 6.378582 CACCAAACATGTTTAACGCTCTAAT 58.621 36.000 22.87 0.00 0.00 1.73
4000 4086 6.861055 CACCAAACATGTTTAACGCTCTAATT 59.139 34.615 22.87 0.00 0.00 1.40
4001 4087 8.018520 CACCAAACATGTTTAACGCTCTAATTA 58.981 33.333 22.87 0.00 0.00 1.40
4002 4088 8.019094 ACCAAACATGTTTAACGCTCTAATTAC 58.981 33.333 22.87 0.00 0.00 1.89
4003 4089 7.483691 CCAAACATGTTTAACGCTCTAATTACC 59.516 37.037 22.87 0.00 0.00 2.85
4004 4090 6.673154 ACATGTTTAACGCTCTAATTACCC 57.327 37.500 0.00 0.00 0.00 3.69
4005 4091 6.174760 ACATGTTTAACGCTCTAATTACCCA 58.825 36.000 0.00 0.00 0.00 4.51
4006 4092 6.093082 ACATGTTTAACGCTCTAATTACCCAC 59.907 38.462 0.00 0.00 0.00 4.61
4007 4093 4.937015 TGTTTAACGCTCTAATTACCCACC 59.063 41.667 0.00 0.00 0.00 4.61
4008 4094 4.822685 TTAACGCTCTAATTACCCACCA 57.177 40.909 0.00 0.00 0.00 4.17
4009 4095 2.685850 ACGCTCTAATTACCCACCAC 57.314 50.000 0.00 0.00 0.00 4.16
4010 4096 2.185387 ACGCTCTAATTACCCACCACT 58.815 47.619 0.00 0.00 0.00 4.00
4011 4097 2.093658 ACGCTCTAATTACCCACCACTG 60.094 50.000 0.00 0.00 0.00 3.66
4012 4098 2.289565 GCTCTAATTACCCACCACTGC 58.710 52.381 0.00 0.00 0.00 4.40
4013 4099 2.919228 CTCTAATTACCCACCACTGCC 58.081 52.381 0.00 0.00 0.00 4.85
4014 4100 2.238646 CTCTAATTACCCACCACTGCCA 59.761 50.000 0.00 0.00 0.00 4.92
4015 4101 2.849943 TCTAATTACCCACCACTGCCAT 59.150 45.455 0.00 0.00 0.00 4.40
4016 4102 2.621556 AATTACCCACCACTGCCATT 57.378 45.000 0.00 0.00 0.00 3.16
4017 4103 1.851304 ATTACCCACCACTGCCATTG 58.149 50.000 0.00 0.00 0.00 2.82
4018 4104 0.251564 TTACCCACCACTGCCATTGG 60.252 55.000 0.00 0.00 40.32 3.16
4020 4106 1.533753 CCCACCACTGCCATTGGTT 60.534 57.895 3.63 0.00 45.62 3.67
4021 4107 0.251564 CCCACCACTGCCATTGGTTA 60.252 55.000 3.63 0.00 45.62 2.85
4022 4108 1.619432 CCCACCACTGCCATTGGTTAT 60.619 52.381 3.63 0.00 45.62 1.89
4023 4109 2.357673 CCCACCACTGCCATTGGTTATA 60.358 50.000 3.63 0.00 45.62 0.98
4024 4110 3.360867 CCACCACTGCCATTGGTTATAA 58.639 45.455 3.63 0.00 45.62 0.98
4025 4111 3.766591 CCACCACTGCCATTGGTTATAAA 59.233 43.478 3.63 0.00 45.62 1.40
4026 4112 4.381505 CCACCACTGCCATTGGTTATAAAC 60.382 45.833 3.63 0.00 45.62 2.01
4027 4113 4.219507 CACCACTGCCATTGGTTATAAACA 59.780 41.667 3.63 0.00 45.62 2.83
4028 4114 4.219725 ACCACTGCCATTGGTTATAAACAC 59.780 41.667 1.72 0.00 45.62 3.32
4029 4115 4.411327 CACTGCCATTGGTTATAAACACG 58.589 43.478 1.72 0.00 0.00 4.49
4030 4116 4.076394 ACTGCCATTGGTTATAAACACGT 58.924 39.130 1.72 0.00 0.00 4.49
4031 4117 4.521256 ACTGCCATTGGTTATAAACACGTT 59.479 37.500 1.72 0.00 0.00 3.99
4032 4118 5.010213 ACTGCCATTGGTTATAAACACGTTT 59.990 36.000 1.72 0.22 36.63 3.60
4033 4119 5.223382 TGCCATTGGTTATAAACACGTTTG 58.777 37.500 1.72 0.00 34.23 2.93
4034 4120 4.623595 GCCATTGGTTATAAACACGTTTGG 59.376 41.667 1.72 9.21 34.23 3.28
4035 4121 5.565045 GCCATTGGTTATAAACACGTTTGGA 60.565 40.000 18.38 0.00 34.23 3.53
4036 4122 5.859648 CCATTGGTTATAAACACGTTTGGAC 59.140 40.000 1.72 1.93 34.23 4.02
4037 4123 6.294286 CCATTGGTTATAAACACGTTTGGACT 60.294 38.462 1.72 0.00 34.23 3.85
4038 4124 5.927954 TGGTTATAAACACGTTTGGACTC 57.072 39.130 0.00 0.00 34.23 3.36
4039 4125 5.366460 TGGTTATAAACACGTTTGGACTCA 58.634 37.500 0.00 0.00 34.23 3.41
4040 4126 5.821470 TGGTTATAAACACGTTTGGACTCAA 59.179 36.000 0.00 0.00 34.23 3.02
4041 4127 6.487331 TGGTTATAAACACGTTTGGACTCAAT 59.513 34.615 0.00 0.00 34.23 2.57
4042 4128 6.799925 GGTTATAAACACGTTTGGACTCAATG 59.200 38.462 5.42 0.00 34.23 2.82
4043 4129 2.774439 AACACGTTTGGACTCAATGC 57.226 45.000 0.00 0.00 32.28 3.56
4044 4130 1.967319 ACACGTTTGGACTCAATGCT 58.033 45.000 0.00 0.00 32.28 3.79
4045 4131 3.120321 ACACGTTTGGACTCAATGCTA 57.880 42.857 0.00 0.00 32.28 3.49
4046 4132 3.674997 ACACGTTTGGACTCAATGCTAT 58.325 40.909 0.00 0.00 32.28 2.97
4047 4133 3.684788 ACACGTTTGGACTCAATGCTATC 59.315 43.478 0.00 0.00 32.28 2.08
4048 4134 3.063997 CACGTTTGGACTCAATGCTATCC 59.936 47.826 0.00 0.00 32.28 2.59
4049 4135 2.614057 CGTTTGGACTCAATGCTATCCC 59.386 50.000 0.00 0.00 32.28 3.85
4050 4136 3.682718 CGTTTGGACTCAATGCTATCCCT 60.683 47.826 0.00 0.00 32.28 4.20
4051 4137 4.273318 GTTTGGACTCAATGCTATCCCTT 58.727 43.478 0.00 0.00 32.28 3.95
4052 4138 3.565764 TGGACTCAATGCTATCCCTTG 57.434 47.619 0.00 0.00 0.00 3.61
4053 4139 3.114606 TGGACTCAATGCTATCCCTTGA 58.885 45.455 0.00 0.00 0.00 3.02
4054 4140 3.523157 TGGACTCAATGCTATCCCTTGAA 59.477 43.478 0.00 0.00 0.00 2.69
4055 4141 4.018506 TGGACTCAATGCTATCCCTTGAAA 60.019 41.667 0.00 0.00 0.00 2.69
4056 4142 5.136105 GGACTCAATGCTATCCCTTGAAAT 58.864 41.667 0.00 0.00 0.00 2.17
4057 4143 5.240403 GGACTCAATGCTATCCCTTGAAATC 59.760 44.000 0.00 0.00 0.00 2.17
4058 4144 6.011122 ACTCAATGCTATCCCTTGAAATCT 57.989 37.500 0.00 0.00 0.00 2.40
4059 4145 5.826737 ACTCAATGCTATCCCTTGAAATCTG 59.173 40.000 0.00 0.00 0.00 2.90
4060 4146 4.581824 TCAATGCTATCCCTTGAAATCTGC 59.418 41.667 0.00 0.00 0.00 4.26
4061 4147 2.936202 TGCTATCCCTTGAAATCTGCC 58.064 47.619 0.00 0.00 0.00 4.85
4062 4148 2.241941 TGCTATCCCTTGAAATCTGCCA 59.758 45.455 0.00 0.00 0.00 4.92
4063 4149 3.117398 TGCTATCCCTTGAAATCTGCCAT 60.117 43.478 0.00 0.00 0.00 4.40
4064 4150 3.255149 GCTATCCCTTGAAATCTGCCATG 59.745 47.826 0.00 0.00 0.00 3.66
4065 4151 2.905415 TCCCTTGAAATCTGCCATGT 57.095 45.000 0.00 0.00 0.00 3.21
4066 4152 4.524802 ATCCCTTGAAATCTGCCATGTA 57.475 40.909 0.00 0.00 0.00 2.29
4067 4153 4.314522 TCCCTTGAAATCTGCCATGTAA 57.685 40.909 0.00 0.00 0.00 2.41
4068 4154 4.870636 TCCCTTGAAATCTGCCATGTAAT 58.129 39.130 0.00 0.00 0.00 1.89
4069 4155 5.271598 TCCCTTGAAATCTGCCATGTAATT 58.728 37.500 0.00 0.00 0.00 1.40
4070 4156 6.430864 TCCCTTGAAATCTGCCATGTAATTA 58.569 36.000 0.00 0.00 0.00 1.40
4071 4157 6.894654 TCCCTTGAAATCTGCCATGTAATTAA 59.105 34.615 0.00 0.00 0.00 1.40
4072 4158 7.564660 TCCCTTGAAATCTGCCATGTAATTAAT 59.435 33.333 0.00 0.00 0.00 1.40
4073 4159 8.859090 CCCTTGAAATCTGCCATGTAATTAATA 58.141 33.333 0.00 0.00 0.00 0.98
4077 4163 9.812347 TGAAATCTGCCATGTAATTAATATCCT 57.188 29.630 0.00 0.00 0.00 3.24
4095 4181 8.904099 AATATCCTACTATTCCCACGAAAAAG 57.096 34.615 0.00 0.00 0.00 2.27
4096 4182 5.750352 TCCTACTATTCCCACGAAAAAGT 57.250 39.130 0.00 0.00 34.45 2.66
4097 4183 6.855763 TCCTACTATTCCCACGAAAAAGTA 57.144 37.500 0.00 0.00 33.04 2.24
4098 4184 7.243604 TCCTACTATTCCCACGAAAAAGTAA 57.756 36.000 0.00 0.00 33.53 2.24
4099 4185 7.854337 TCCTACTATTCCCACGAAAAAGTAAT 58.146 34.615 0.00 0.00 33.53 1.89
4100 4186 8.323567 TCCTACTATTCCCACGAAAAAGTAATT 58.676 33.333 0.00 0.00 33.53 1.40
4101 4187 8.395633 CCTACTATTCCCACGAAAAAGTAATTG 58.604 37.037 0.00 0.00 33.53 2.32
4102 4188 7.989416 ACTATTCCCACGAAAAAGTAATTGA 57.011 32.000 0.00 0.00 30.51 2.57
4103 4189 8.575649 ACTATTCCCACGAAAAAGTAATTGAT 57.424 30.769 0.00 0.00 30.51 2.57
4104 4190 9.675464 ACTATTCCCACGAAAAAGTAATTGATA 57.325 29.630 0.00 0.00 30.51 2.15
4107 4193 8.801882 TTCCCACGAAAAAGTAATTGATATCT 57.198 30.769 3.98 0.00 0.00 1.98
4108 4194 8.801882 TCCCACGAAAAAGTAATTGATATCTT 57.198 30.769 3.98 0.00 0.00 2.40
4109 4195 9.893634 TCCCACGAAAAAGTAATTGATATCTTA 57.106 29.630 3.98 0.00 0.00 2.10
4110 4196 9.931210 CCCACGAAAAAGTAATTGATATCTTAC 57.069 33.333 3.98 5.62 0.00 2.34
4111 4197 9.931210 CCACGAAAAAGTAATTGATATCTTACC 57.069 33.333 3.98 0.00 0.00 2.85
4129 4215 8.780846 ATCTTACCAAATATCAACGTACAACA 57.219 30.769 0.00 0.00 0.00 3.33
4130 4216 8.604640 TCTTACCAAATATCAACGTACAACAA 57.395 30.769 0.00 0.00 0.00 2.83
4131 4217 9.053840 TCTTACCAAATATCAACGTACAACAAA 57.946 29.630 0.00 0.00 0.00 2.83
4132 4218 9.834628 CTTACCAAATATCAACGTACAACAAAT 57.165 29.630 0.00 0.00 0.00 2.32
4188 4274 7.956420 TCCTACCTAATATAAACGTGCATTG 57.044 36.000 0.00 0.00 0.00 2.82
4189 4275 6.425721 TCCTACCTAATATAAACGTGCATTGC 59.574 38.462 0.46 0.46 0.00 3.56
4190 4276 6.203915 CCTACCTAATATAAACGTGCATTGCA 59.796 38.462 7.38 7.38 35.60 4.08
4206 4292 7.172654 TGCATTGCACGTACATTATTACTAG 57.827 36.000 7.38 0.00 31.71 2.57
4207 4293 6.759356 TGCATTGCACGTACATTATTACTAGT 59.241 34.615 7.38 0.00 31.71 2.57
4622 4708 4.446311 GGGCATGTATACTCCAATTGACCT 60.446 45.833 7.12 0.00 0.00 3.85
4899 5014 8.707938 AATATGCAAAATTGAAGAGGTTTAGC 57.292 30.769 0.00 0.00 0.00 3.09
4902 5017 6.581712 TGCAAAATTGAAGAGGTTTAGCTTT 58.418 32.000 0.00 0.00 0.00 3.51
4962 5077 4.866486 GCCCTCTATTTTCATTTGCAACTG 59.134 41.667 10.37 10.37 0.00 3.16
5030 5145 5.913137 ATGAAAATACAGCCGAATCCAAA 57.087 34.783 0.00 0.00 0.00 3.28
5091 5206 3.002965 CACTTACCGAAAAAGGCTTTCGT 59.997 43.478 13.76 9.60 46.85 3.85
5103 5218 2.093341 AGGCTTTCGTCCCGCTTTATAA 60.093 45.455 0.00 0.00 0.00 0.98
5173 5308 4.021894 AGGTCTAACACAGCAAGTAGTCAG 60.022 45.833 0.00 0.00 0.00 3.51
5259 5400 1.156736 GTGCGGCACAACATCTAGTT 58.843 50.000 27.10 0.00 42.42 2.24
5377 5518 4.899239 CTAAGCGGCCGCCAGAGG 62.899 72.222 44.47 26.02 43.17 3.69
5388 5529 0.108186 CGCCAGAGGTGCAAGTATCA 60.108 55.000 0.00 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
222 271 0.919710 CCTCGATTCCCCTTTCCCTT 59.080 55.000 0.00 0.00 0.00 3.95
316 370 0.333993 TCTTACCCCTGCTAGGACGT 59.666 55.000 0.00 0.00 37.67 4.34
336 390 3.469008 AACTGTGACTGGAAATGTCGA 57.531 42.857 0.00 0.00 37.26 4.20
363 417 6.019075 CACATCTGTCAGTTTTTGTCGTTAGA 60.019 38.462 0.00 0.00 0.00 2.10
398 452 6.279513 TGACACCACAACTTCATTTTCTTT 57.720 33.333 0.00 0.00 0.00 2.52
470 530 4.500035 GGCGAGAGAATTCCTTATTCGACT 60.500 45.833 14.68 0.00 45.99 4.18
474 534 7.730364 TTATTGGCGAGAGAATTCCTTATTC 57.270 36.000 0.65 0.00 42.51 1.75
492 552 3.119849 CCTCGAACCTTGCAGTTTATTGG 60.120 47.826 0.00 0.00 0.00 3.16
493 553 3.670627 GCCTCGAACCTTGCAGTTTATTG 60.671 47.826 0.00 0.00 0.00 1.90
494 554 2.488153 GCCTCGAACCTTGCAGTTTATT 59.512 45.455 0.00 0.00 0.00 1.40
495 555 2.084546 GCCTCGAACCTTGCAGTTTAT 58.915 47.619 0.00 0.00 0.00 1.40
496 556 1.519408 GCCTCGAACCTTGCAGTTTA 58.481 50.000 0.00 0.00 0.00 2.01
497 557 1.507141 CGCCTCGAACCTTGCAGTTT 61.507 55.000 0.00 0.00 0.00 2.66
498 558 1.961277 CGCCTCGAACCTTGCAGTT 60.961 57.895 0.00 0.00 0.00 3.16
499 559 2.357517 CGCCTCGAACCTTGCAGT 60.358 61.111 0.00 0.00 0.00 4.40
565 625 0.680280 GAGGAGAGACAGGGTGCGTA 60.680 60.000 0.00 0.00 0.00 4.42
583 643 2.241176 GAGAGAGAGACTGGGGAAGAGA 59.759 54.545 0.00 0.00 0.00 3.10
604 666 2.498078 GTGTGGGTAGAGAAAGGGAGAG 59.502 54.545 0.00 0.00 0.00 3.20
605 667 2.537143 GTGTGGGTAGAGAAAGGGAGA 58.463 52.381 0.00 0.00 0.00 3.71
606 668 1.555533 GGTGTGGGTAGAGAAAGGGAG 59.444 57.143 0.00 0.00 0.00 4.30
607 669 1.132657 TGGTGTGGGTAGAGAAAGGGA 60.133 52.381 0.00 0.00 0.00 4.20
608 670 1.358152 TGGTGTGGGTAGAGAAAGGG 58.642 55.000 0.00 0.00 0.00 3.95
609 671 2.552373 GGTTGGTGTGGGTAGAGAAAGG 60.552 54.545 0.00 0.00 0.00 3.11
610 672 2.552373 GGGTTGGTGTGGGTAGAGAAAG 60.552 54.545 0.00 0.00 0.00 2.62
611 673 1.422402 GGGTTGGTGTGGGTAGAGAAA 59.578 52.381 0.00 0.00 0.00 2.52
612 674 1.061546 GGGTTGGTGTGGGTAGAGAA 58.938 55.000 0.00 0.00 0.00 2.87
613 675 0.838987 GGGGTTGGTGTGGGTAGAGA 60.839 60.000 0.00 0.00 0.00 3.10
925 990 1.074319 GCGAAATCAGCGACGGTACA 61.074 55.000 0.00 0.00 0.00 2.90
981 1046 1.204786 TTCCGATGCTCCCCTCCAAA 61.205 55.000 0.00 0.00 0.00 3.28
1166 1231 7.302524 GGAGCTATCAATCAAACGTACAAAAA 58.697 34.615 0.00 0.00 0.00 1.94
1333 1399 5.464069 TCCAGAGCTGTGAGGGTTATATTA 58.536 41.667 13.38 0.00 0.00 0.98
1343 1409 2.827800 TTCAGTTCCAGAGCTGTGAG 57.172 50.000 13.38 2.63 40.07 3.51
1475 1542 0.329596 ATCACTGCCTCCCAAGAACC 59.670 55.000 0.00 0.00 0.00 3.62
1955 2037 4.377021 ACGACAATCACAAGCTACAAGAA 58.623 39.130 0.00 0.00 0.00 2.52
2086 2168 6.845758 TCCAGATCATTTTCTTTCATGCTT 57.154 33.333 0.00 0.00 0.00 3.91
2215 2297 8.767478 ACACCATAACTACGTAATATAATGCC 57.233 34.615 0.00 0.00 0.00 4.40
2253 2335 6.268566 ACTTTTGACAAGCAACAGAGAAATC 58.731 36.000 0.00 0.00 36.59 2.17
2292 2374 8.850156 CAAAGGAAAAGAAATGGTAGAGAGAAA 58.150 33.333 0.00 0.00 0.00 2.52
2341 2423 0.107831 GCTTGTACCACAGACCACCA 59.892 55.000 0.00 0.00 0.00 4.17
2361 2443 3.125829 TGAAGCTCGTCAAATTGATCTGC 59.874 43.478 0.00 4.16 0.00 4.26
2523 2609 9.508642 AAAGAATTGTTTTGGACTTTTGGTTAA 57.491 25.926 0.00 0.00 0.00 2.01
2950 3036 1.523938 GGGTAAGCGAGCCATGGAC 60.524 63.158 18.40 7.03 45.84 4.02
3151 3237 3.181480 TGCCAAGTCTTTTGTTAAGTGCC 60.181 43.478 0.00 0.00 0.00 5.01
3152 3238 4.040445 TGCCAAGTCTTTTGTTAAGTGC 57.960 40.909 0.00 0.00 0.00 4.40
3248 3334 2.153645 TGTGAGCATGCCAACAAGTAG 58.846 47.619 15.66 0.00 0.00 2.57
3430 3516 6.630444 TTACGTCCTACAGAAGCCTTATAG 57.370 41.667 0.00 0.00 0.00 1.31
3436 3522 3.858247 ACAATTACGTCCTACAGAAGCC 58.142 45.455 0.00 0.00 0.00 4.35
3755 3841 0.732880 CGTTAGCCTCCACAGTGTCG 60.733 60.000 0.00 0.00 0.00 4.35
3882 3968 9.509956 CCATTCGGGTCTTTTTATATTGGTATA 57.490 33.333 0.00 0.00 0.00 1.47
3883 3969 8.404107 CCATTCGGGTCTTTTTATATTGGTAT 57.596 34.615 0.00 0.00 0.00 2.73
3884 3970 7.811117 CCATTCGGGTCTTTTTATATTGGTA 57.189 36.000 0.00 0.00 0.00 3.25
3885 3971 6.709018 CCATTCGGGTCTTTTTATATTGGT 57.291 37.500 0.00 0.00 0.00 3.67
3901 3987 0.740737 GTTTGGATCTGCCCATTCGG 59.259 55.000 0.00 0.00 35.87 4.30
3902 3988 0.740737 GGTTTGGATCTGCCCATTCG 59.259 55.000 0.00 0.00 35.87 3.34
3903 3989 1.851304 TGGTTTGGATCTGCCCATTC 58.149 50.000 0.00 0.00 35.87 2.67
3904 3990 2.023695 AGATGGTTTGGATCTGCCCATT 60.024 45.455 7.74 0.00 36.08 3.16
3905 3991 1.572415 AGATGGTTTGGATCTGCCCAT 59.428 47.619 6.49 6.49 38.58 4.00
3906 3992 1.002069 AGATGGTTTGGATCTGCCCA 58.998 50.000 0.00 0.00 34.97 5.36
3907 3993 1.753073 CAAGATGGTTTGGATCTGCCC 59.247 52.381 0.00 0.00 34.97 5.36
3908 3994 2.424956 GTCAAGATGGTTTGGATCTGCC 59.575 50.000 0.00 0.00 30.30 4.85
3909 3995 2.424956 GGTCAAGATGGTTTGGATCTGC 59.575 50.000 0.00 0.00 30.30 4.26
3910 3996 2.679837 CGGTCAAGATGGTTTGGATCTG 59.320 50.000 0.00 0.00 30.30 2.90
3911 3997 2.305927 ACGGTCAAGATGGTTTGGATCT 59.694 45.455 0.00 0.00 0.00 2.75
3912 3998 2.678336 GACGGTCAAGATGGTTTGGATC 59.322 50.000 2.62 0.00 0.00 3.36
3913 3999 2.039746 TGACGGTCAAGATGGTTTGGAT 59.960 45.455 8.68 0.00 0.00 3.41
3914 4000 1.418264 TGACGGTCAAGATGGTTTGGA 59.582 47.619 8.68 0.00 0.00 3.53
3915 4001 1.890876 TGACGGTCAAGATGGTTTGG 58.109 50.000 8.68 0.00 0.00 3.28
3916 4002 3.980646 TTTGACGGTCAAGATGGTTTG 57.019 42.857 21.47 0.00 37.70 2.93
3917 4003 4.141287 TGATTTGACGGTCAAGATGGTTT 58.859 39.130 21.47 4.56 37.70 3.27
3918 4004 3.750371 TGATTTGACGGTCAAGATGGTT 58.250 40.909 21.47 6.08 37.70 3.67
3919 4005 3.417069 TGATTTGACGGTCAAGATGGT 57.583 42.857 21.47 8.59 37.70 3.55
3920 4006 3.691118 ACATGATTTGACGGTCAAGATGG 59.309 43.478 26.33 18.57 37.70 3.51
3921 4007 4.952262 ACATGATTTGACGGTCAAGATG 57.048 40.909 21.47 22.91 37.70 2.90
3922 4008 7.050377 AGATAACATGATTTGACGGTCAAGAT 58.950 34.615 21.47 17.34 37.70 2.40
3923 4009 6.406370 AGATAACATGATTTGACGGTCAAGA 58.594 36.000 21.47 13.93 37.70 3.02
3924 4010 6.668541 AGATAACATGATTTGACGGTCAAG 57.331 37.500 21.47 13.21 37.70 3.02
3925 4011 7.201487 CGTTAGATAACATGATTTGACGGTCAA 60.201 37.037 19.07 19.07 35.99 3.18
3926 4012 6.254804 CGTTAGATAACATGATTTGACGGTCA 59.745 38.462 6.76 6.76 35.99 4.02
3927 4013 6.292168 CCGTTAGATAACATGATTTGACGGTC 60.292 42.308 0.00 0.00 40.82 4.79
3928 4014 5.522460 CCGTTAGATAACATGATTTGACGGT 59.478 40.000 0.00 0.00 40.82 4.83
3929 4015 5.974300 CCGTTAGATAACATGATTTGACGG 58.026 41.667 0.00 3.34 40.02 4.79
3930 4016 6.583912 ACCGTTAGATAACATGATTTGACG 57.416 37.500 0.00 0.00 35.99 4.35
3931 4017 7.970384 TCAACCGTTAGATAACATGATTTGAC 58.030 34.615 0.00 0.00 35.99 3.18
3932 4018 8.554835 TTCAACCGTTAGATAACATGATTTGA 57.445 30.769 0.00 0.00 35.99 2.69
3933 4019 9.787532 ATTTCAACCGTTAGATAACATGATTTG 57.212 29.630 0.00 0.00 35.99 2.32
3935 4021 8.335356 CGATTTCAACCGTTAGATAACATGATT 58.665 33.333 0.00 0.00 35.99 2.57
3936 4022 7.518370 GCGATTTCAACCGTTAGATAACATGAT 60.518 37.037 0.00 0.00 35.99 2.45
3937 4023 6.237996 GCGATTTCAACCGTTAGATAACATGA 60.238 38.462 0.00 2.28 35.99 3.07
3938 4024 5.901884 GCGATTTCAACCGTTAGATAACATG 59.098 40.000 3.81 0.00 35.99 3.21
3939 4025 5.815740 AGCGATTTCAACCGTTAGATAACAT 59.184 36.000 3.81 0.00 35.99 2.71
3940 4026 5.172934 AGCGATTTCAACCGTTAGATAACA 58.827 37.500 3.81 0.00 35.99 2.41
3941 4027 5.713822 AGCGATTTCAACCGTTAGATAAC 57.286 39.130 0.00 0.00 0.00 1.89
3942 4028 5.870433 TGAAGCGATTTCAACCGTTAGATAA 59.130 36.000 0.00 0.00 42.69 1.75
3943 4029 5.412640 TGAAGCGATTTCAACCGTTAGATA 58.587 37.500 0.00 0.00 42.69 1.98
3944 4030 4.250464 TGAAGCGATTTCAACCGTTAGAT 58.750 39.130 0.00 0.00 42.69 1.98
3945 4031 3.655486 TGAAGCGATTTCAACCGTTAGA 58.345 40.909 0.00 0.00 42.69 2.10
3954 4040 3.252944 TGCTCAACATTGAAGCGATTTCA 59.747 39.130 0.00 0.00 43.92 2.69
3955 4041 3.605486 GTGCTCAACATTGAAGCGATTTC 59.395 43.478 0.00 0.00 36.64 2.17
3956 4042 3.568538 GTGCTCAACATTGAAGCGATTT 58.431 40.909 0.00 0.00 36.64 2.17
3957 4043 2.095059 GGTGCTCAACATTGAAGCGATT 60.095 45.455 0.00 0.00 36.64 3.34
3958 4044 1.470098 GGTGCTCAACATTGAAGCGAT 59.530 47.619 0.00 0.00 36.64 4.58
3959 4045 0.874390 GGTGCTCAACATTGAAGCGA 59.126 50.000 0.00 0.00 36.64 4.93
3960 4046 0.592637 TGGTGCTCAACATTGAAGCG 59.407 50.000 0.00 0.00 36.64 4.68
3961 4047 2.796593 GTTTGGTGCTCAACATTGAAGC 59.203 45.455 0.00 3.10 36.64 3.86
3962 4048 4.044336 TGTTTGGTGCTCAACATTGAAG 57.956 40.909 0.00 0.00 36.64 3.02
3963 4049 4.141981 ACATGTTTGGTGCTCAACATTGAA 60.142 37.500 0.00 0.00 36.64 2.69
3964 4050 3.384146 ACATGTTTGGTGCTCAACATTGA 59.616 39.130 0.00 0.00 34.67 2.57
3965 4051 3.719924 ACATGTTTGGTGCTCAACATTG 58.280 40.909 0.00 2.71 34.67 2.82
3966 4052 4.405116 AACATGTTTGGTGCTCAACATT 57.595 36.364 4.92 0.00 34.67 2.71
3967 4053 4.405116 AAACATGTTTGGTGCTCAACAT 57.595 36.364 22.71 0.00 34.67 2.71
3968 4054 3.883830 AAACATGTTTGGTGCTCAACA 57.116 38.095 22.71 0.00 34.67 3.33
3969 4055 4.206200 CGTTAAACATGTTTGGTGCTCAAC 59.794 41.667 29.72 21.95 34.67 3.18
3970 4056 4.355437 CGTTAAACATGTTTGGTGCTCAA 58.645 39.130 29.72 13.89 34.23 3.02
3971 4057 3.793801 GCGTTAAACATGTTTGGTGCTCA 60.794 43.478 29.72 8.67 34.23 4.26
3972 4058 2.724174 GCGTTAAACATGTTTGGTGCTC 59.276 45.455 29.72 12.48 34.23 4.26
3973 4059 2.360801 AGCGTTAAACATGTTTGGTGCT 59.639 40.909 29.72 27.92 34.23 4.40
3974 4060 2.724174 GAGCGTTAAACATGTTTGGTGC 59.276 45.455 29.72 26.52 34.23 5.01
3975 4061 4.223320 AGAGCGTTAAACATGTTTGGTG 57.777 40.909 29.72 19.84 34.23 4.17
3976 4062 6.569179 ATTAGAGCGTTAAACATGTTTGGT 57.431 33.333 29.72 19.87 34.23 3.67
3977 4063 7.483691 GGTAATTAGAGCGTTAAACATGTTTGG 59.516 37.037 29.72 19.98 34.23 3.28
3978 4064 7.483691 GGGTAATTAGAGCGTTAAACATGTTTG 59.516 37.037 29.72 16.51 34.23 2.93
3979 4065 7.175293 TGGGTAATTAGAGCGTTAAACATGTTT 59.825 33.333 25.99 25.99 36.63 2.83
3980 4066 6.655848 TGGGTAATTAGAGCGTTAAACATGTT 59.344 34.615 4.92 4.92 0.00 2.71
3981 4067 6.093082 GTGGGTAATTAGAGCGTTAAACATGT 59.907 38.462 0.00 0.00 0.00 3.21
3982 4068 6.457799 GGTGGGTAATTAGAGCGTTAAACATG 60.458 42.308 0.00 0.00 0.00 3.21
3983 4069 5.587443 GGTGGGTAATTAGAGCGTTAAACAT 59.413 40.000 0.00 0.00 0.00 2.71
3984 4070 4.937015 GGTGGGTAATTAGAGCGTTAAACA 59.063 41.667 0.00 0.00 0.00 2.83
3985 4071 4.937015 TGGTGGGTAATTAGAGCGTTAAAC 59.063 41.667 0.00 0.00 0.00 2.01
3986 4072 4.937015 GTGGTGGGTAATTAGAGCGTTAAA 59.063 41.667 0.00 0.00 0.00 1.52
3987 4073 4.223477 AGTGGTGGGTAATTAGAGCGTTAA 59.777 41.667 0.00 0.00 0.00 2.01
3988 4074 3.770933 AGTGGTGGGTAATTAGAGCGTTA 59.229 43.478 0.00 0.00 0.00 3.18
3989 4075 2.570302 AGTGGTGGGTAATTAGAGCGTT 59.430 45.455 0.00 0.00 0.00 4.84
3990 4076 2.093658 CAGTGGTGGGTAATTAGAGCGT 60.094 50.000 0.00 0.00 0.00 5.07
3991 4077 2.550978 CAGTGGTGGGTAATTAGAGCG 58.449 52.381 0.00 0.00 0.00 5.03
3992 4078 2.289565 GCAGTGGTGGGTAATTAGAGC 58.710 52.381 0.00 0.00 0.00 4.09
3993 4079 2.238646 TGGCAGTGGTGGGTAATTAGAG 59.761 50.000 0.00 0.00 0.00 2.43
3994 4080 2.270858 TGGCAGTGGTGGGTAATTAGA 58.729 47.619 0.00 0.00 0.00 2.10
3995 4081 2.799126 TGGCAGTGGTGGGTAATTAG 57.201 50.000 0.00 0.00 0.00 1.73
3996 4082 3.360867 CAATGGCAGTGGTGGGTAATTA 58.639 45.455 7.12 0.00 0.00 1.40
3997 4083 2.178580 CAATGGCAGTGGTGGGTAATT 58.821 47.619 7.12 0.00 0.00 1.40
3998 4084 1.619432 CCAATGGCAGTGGTGGGTAAT 60.619 52.381 25.07 0.00 0.00 1.89
3999 4085 0.251564 CCAATGGCAGTGGTGGGTAA 60.252 55.000 25.07 0.00 0.00 2.85
4000 4086 1.382240 CCAATGGCAGTGGTGGGTA 59.618 57.895 25.07 0.00 0.00 3.69
4001 4087 2.118076 CCAATGGCAGTGGTGGGT 59.882 61.111 25.07 0.00 0.00 4.51
4006 4092 4.674101 CGTGTTTATAACCAATGGCAGTGG 60.674 45.833 30.65 30.65 42.28 4.00
4007 4093 4.083003 ACGTGTTTATAACCAATGGCAGTG 60.083 41.667 8.18 8.18 0.00 3.66
4008 4094 4.076394 ACGTGTTTATAACCAATGGCAGT 58.924 39.130 0.00 0.00 0.00 4.40
4009 4095 4.695217 ACGTGTTTATAACCAATGGCAG 57.305 40.909 0.00 0.00 0.00 4.85
4010 4096 5.223382 CAAACGTGTTTATAACCAATGGCA 58.777 37.500 0.00 0.00 0.00 4.92
4011 4097 4.623595 CCAAACGTGTTTATAACCAATGGC 59.376 41.667 0.00 0.00 0.00 4.40
4012 4098 5.859648 GTCCAAACGTGTTTATAACCAATGG 59.140 40.000 0.00 0.00 0.00 3.16
4013 4099 6.674066 AGTCCAAACGTGTTTATAACCAATG 58.326 36.000 0.00 0.00 0.00 2.82
4014 4100 6.487331 TGAGTCCAAACGTGTTTATAACCAAT 59.513 34.615 0.00 0.00 0.00 3.16
4015 4101 5.821470 TGAGTCCAAACGTGTTTATAACCAA 59.179 36.000 0.00 0.00 0.00 3.67
4016 4102 5.366460 TGAGTCCAAACGTGTTTATAACCA 58.634 37.500 0.00 0.00 0.00 3.67
4017 4103 5.927954 TGAGTCCAAACGTGTTTATAACC 57.072 39.130 0.00 0.00 0.00 2.85
4018 4104 6.304683 GCATTGAGTCCAAACGTGTTTATAAC 59.695 38.462 0.00 0.00 35.67 1.89
4019 4105 6.205853 AGCATTGAGTCCAAACGTGTTTATAA 59.794 34.615 0.00 0.00 35.67 0.98
4020 4106 5.703592 AGCATTGAGTCCAAACGTGTTTATA 59.296 36.000 0.00 0.00 35.67 0.98
4021 4107 4.518970 AGCATTGAGTCCAAACGTGTTTAT 59.481 37.500 0.00 0.00 35.67 1.40
4022 4108 3.880490 AGCATTGAGTCCAAACGTGTTTA 59.120 39.130 0.00 0.00 35.67 2.01
4023 4109 2.687935 AGCATTGAGTCCAAACGTGTTT 59.312 40.909 0.00 0.00 35.67 2.83
4024 4110 2.297701 AGCATTGAGTCCAAACGTGTT 58.702 42.857 0.00 0.00 35.67 3.32
4025 4111 1.967319 AGCATTGAGTCCAAACGTGT 58.033 45.000 0.00 0.00 35.67 4.49
4026 4112 3.063997 GGATAGCATTGAGTCCAAACGTG 59.936 47.826 0.00 0.00 35.67 4.49
4027 4113 3.270877 GGATAGCATTGAGTCCAAACGT 58.729 45.455 0.00 0.00 35.67 3.99
4028 4114 2.614057 GGGATAGCATTGAGTCCAAACG 59.386 50.000 0.00 0.00 35.67 3.60
4029 4115 3.891049 AGGGATAGCATTGAGTCCAAAC 58.109 45.455 0.00 0.00 35.67 2.93
4030 4116 4.018506 TCAAGGGATAGCATTGAGTCCAAA 60.019 41.667 0.00 0.00 35.67 3.28
4031 4117 3.523157 TCAAGGGATAGCATTGAGTCCAA 59.477 43.478 0.00 0.00 36.61 3.53
4032 4118 3.114606 TCAAGGGATAGCATTGAGTCCA 58.885 45.455 0.00 0.00 32.31 4.02
4033 4119 3.845781 TCAAGGGATAGCATTGAGTCC 57.154 47.619 0.00 0.00 0.00 3.85
4034 4120 6.017275 CAGATTTCAAGGGATAGCATTGAGTC 60.017 42.308 0.00 0.00 34.64 3.36
4035 4121 5.826737 CAGATTTCAAGGGATAGCATTGAGT 59.173 40.000 0.00 0.00 34.64 3.41
4036 4122 5.278364 GCAGATTTCAAGGGATAGCATTGAG 60.278 44.000 0.00 0.00 34.64 3.02
4037 4123 4.581824 GCAGATTTCAAGGGATAGCATTGA 59.418 41.667 0.00 0.00 0.00 2.57
4038 4124 4.261909 GGCAGATTTCAAGGGATAGCATTG 60.262 45.833 0.00 0.00 0.00 2.82
4039 4125 3.893813 GGCAGATTTCAAGGGATAGCATT 59.106 43.478 0.00 0.00 0.00 3.56
4040 4126 3.117398 TGGCAGATTTCAAGGGATAGCAT 60.117 43.478 0.00 0.00 0.00 3.79
4041 4127 2.241941 TGGCAGATTTCAAGGGATAGCA 59.758 45.455 0.00 0.00 0.00 3.49
4042 4128 2.936202 TGGCAGATTTCAAGGGATAGC 58.064 47.619 0.00 0.00 0.00 2.97
4043 4129 4.467769 ACATGGCAGATTTCAAGGGATAG 58.532 43.478 0.00 0.00 0.00 2.08
4044 4130 4.524802 ACATGGCAGATTTCAAGGGATA 57.475 40.909 0.00 0.00 0.00 2.59
4045 4131 3.393426 ACATGGCAGATTTCAAGGGAT 57.607 42.857 0.00 0.00 0.00 3.85
4046 4132 2.905415 ACATGGCAGATTTCAAGGGA 57.095 45.000 0.00 0.00 0.00 4.20
4047 4133 5.603170 AATTACATGGCAGATTTCAAGGG 57.397 39.130 0.00 0.00 0.00 3.95
4051 4137 9.812347 AGGATATTAATTACATGGCAGATTTCA 57.188 29.630 0.00 0.00 0.00 2.69
4069 4155 9.991906 CTTTTTCGTGGGAATAGTAGGATATTA 57.008 33.333 0.00 0.00 30.88 0.98
4070 4156 8.491958 ACTTTTTCGTGGGAATAGTAGGATATT 58.508 33.333 0.00 0.00 30.28 1.28
4071 4157 8.030913 ACTTTTTCGTGGGAATAGTAGGATAT 57.969 34.615 0.00 0.00 30.28 1.63
4072 4158 7.427989 ACTTTTTCGTGGGAATAGTAGGATA 57.572 36.000 0.00 0.00 30.28 2.59
4073 4159 6.309389 ACTTTTTCGTGGGAATAGTAGGAT 57.691 37.500 0.00 0.00 30.28 3.24
4074 4160 5.750352 ACTTTTTCGTGGGAATAGTAGGA 57.250 39.130 0.00 0.00 30.28 2.94
4075 4161 8.395633 CAATTACTTTTTCGTGGGAATAGTAGG 58.604 37.037 0.00 0.00 34.21 3.18
4076 4162 9.158233 TCAATTACTTTTTCGTGGGAATAGTAG 57.842 33.333 0.00 0.00 34.21 2.57
4077 4163 9.675464 ATCAATTACTTTTTCGTGGGAATAGTA 57.325 29.630 0.00 0.00 32.75 1.82
4078 4164 7.989416 TCAATTACTTTTTCGTGGGAATAGT 57.011 32.000 0.00 0.00 34.09 2.12
4081 4167 9.408648 AGATATCAATTACTTTTTCGTGGGAAT 57.591 29.630 5.32 0.00 30.88 3.01
4082 4168 8.801882 AGATATCAATTACTTTTTCGTGGGAA 57.198 30.769 5.32 0.00 0.00 3.97
4083 4169 8.801882 AAGATATCAATTACTTTTTCGTGGGA 57.198 30.769 5.32 0.00 0.00 4.37
4084 4170 9.931210 GTAAGATATCAATTACTTTTTCGTGGG 57.069 33.333 5.32 0.00 0.00 4.61
4085 4171 9.931210 GGTAAGATATCAATTACTTTTTCGTGG 57.069 33.333 5.32 0.00 33.36 4.94
4103 4189 9.872721 TGTTGTACGTTGATATTTGGTAAGATA 57.127 29.630 0.00 0.00 0.00 1.98
4104 4190 8.780846 TGTTGTACGTTGATATTTGGTAAGAT 57.219 30.769 0.00 0.00 0.00 2.40
4105 4191 8.604640 TTGTTGTACGTTGATATTTGGTAAGA 57.395 30.769 0.00 0.00 0.00 2.10
4106 4192 9.834628 ATTTGTTGTACGTTGATATTTGGTAAG 57.165 29.630 0.00 0.00 0.00 2.34
4162 4248 9.647797 CAATGCACGTTTATATTAGGTAGGATA 57.352 33.333 0.00 0.00 0.00 2.59
4163 4249 7.119262 GCAATGCACGTTTATATTAGGTAGGAT 59.881 37.037 0.00 0.00 0.00 3.24
4164 4250 6.425721 GCAATGCACGTTTATATTAGGTAGGA 59.574 38.462 0.00 0.00 0.00 2.94
4165 4251 6.203915 TGCAATGCACGTTTATATTAGGTAGG 59.796 38.462 2.72 0.00 31.71 3.18
4166 4252 7.184800 TGCAATGCACGTTTATATTAGGTAG 57.815 36.000 2.72 0.00 31.71 3.18
4182 4268 6.759356 ACTAGTAATAATGTACGTGCAATGCA 59.241 34.615 11.22 2.72 35.60 3.96
4183 4269 7.173863 ACTAGTAATAATGTACGTGCAATGC 57.826 36.000 11.22 0.00 0.00 3.56
4187 4273 9.506018 TCCTATACTAGTAATAATGTACGTGCA 57.494 33.333 9.28 9.28 0.00 4.57
4222 4308 1.560505 AATCAGTTCAATGTGCCCCC 58.439 50.000 0.00 0.00 0.00 5.40
4375 4461 6.712095 GGAATACATCAAGAGAATGCCATGTA 59.288 38.462 0.00 0.00 32.69 2.29
4622 4708 1.894756 CCGTTGCTTTGGGTCGGAA 60.895 57.895 0.00 0.00 43.22 4.30
4879 4965 7.482654 AAAAGCTAAACCTCTTCAATTTTGC 57.517 32.000 0.00 0.00 35.28 3.68
4916 5031 5.106118 GCCATTCAAAGAACTTAACCTCTCC 60.106 44.000 0.00 0.00 0.00 3.71
4918 5033 4.767409 GGCCATTCAAAGAACTTAACCTCT 59.233 41.667 0.00 0.00 0.00 3.69
5011 5126 5.010282 AGACTTTGGATTCGGCTGTATTTT 58.990 37.500 0.00 0.00 0.00 1.82
5030 5145 6.713731 TCCCTTTCCCTATTTGTTAAGACT 57.286 37.500 0.00 0.00 0.00 3.24
5058 5173 1.338973 TCGGTAAGTGCTTGAACTCGT 59.661 47.619 0.00 0.00 0.00 4.18
5103 5218 5.071653 ACCTTGTTGGATGTTTGGCTTTATT 59.928 36.000 0.00 0.00 39.71 1.40
5173 5308 2.784347 GCCCTCAGCATTAACCCTATC 58.216 52.381 0.00 0.00 42.97 2.08
5377 5518 8.795786 TCTTTAAAATGTGTTGATACTTGCAC 57.204 30.769 0.00 0.00 0.00 4.57
5388 5529 5.446143 TGACGCCATCTTTAAAATGTGTT 57.554 34.783 8.54 0.00 0.00 3.32
5539 5686 2.454832 CTTCCCTGACCTGCTTGCGA 62.455 60.000 0.00 0.00 0.00 5.10


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.